Reading layer `BAS_LIM_DEPARTAMENTO' from data source `C:\Users\Jorge Ruiz\Documents\GitHub\ce4-peru.github.io\dashboard\Limite_departamental' using driver `ESRI Shapefile'
Simple feature collection with 25 features and 4 fields
geometry type:  MULTIPOLYGON
dimension:      XY
bbox:           xmin: -203260.8 ymin: 7964769 xmax: 1190991 ymax: 9995733
epsg (SRID):    32718
proj4string:    +proj=utm +zone=18 +south +datum=WGS84 +units=m +no_defs

---
title: "CE4 - Dashboard COVID-19"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
    source_code: embed
    social: menu
    theme: cosmo
    self_contained: FALSE 
    fig_mobile: TRUE
---



```{r libraries, message=F, warning=F}
library(flexdashboard)
library(rio)
library(tidyverse)
library(XML)
library(httr)
library(RCurl)
library(sf)
library(lubridate)
library(leaflet)
library(colorspace)
library(DT)
library(zoo)
library(slider)
library(plotly)
library(waffle)
library(extrafont)
library(plyr)
library(extrafont)
library(waffle)
library(RColorBrewer)
options(scipen=999)
```

```{r imports, message=F, warning=F}
nac <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true")

deps <- rio::import("https://github.com/jincio/COVID_19_PERU/blob/master/reportes_minsa.xlsx?raw=true", sheet = 2)

pop <- read_csv("data/peru_pop_stratum.csv") %>%
  group_by(dep_adm1) %>%
  dplyr::summarise(pop = sum(N)) %>%
  dplyr::mutate(REGION = toupper(dep_adm1))


Paises_LATAM <- c("Argentina","Bolivia","Brazil","Chile","Colombia","Ecuador","Mexico","Peru","Uruguay","Venezuela")
LATAM <- read_csv ("https://covid.ourworldindata.org/data/owid-covid-data.csv") %>%
  dplyr::filter(location %in% Paises_LATAM) %>%
  dplyr::mutate( mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6))

shp <- st_read("Limite_departamental", stringsAsFactors = F)%>% 
  st_transform(4326) %>% 
  select(Departamento = NOMBDEP)
```


```{r DMdeps, message=F, warning=F}
c.date <- max(deps$Fecha)
y.date <- as.Date(c.date) - 1 
date <- ymd(Sys.Date())


dep <- 
  deps %>% 
  dplyr::select(dat = Fecha,
                dep = REGION, 
                pos = Positivos_totales, 
                pos.imp = PositivosImputados_totales,
                pas =Fallecidos, 
                smp =Total_muestras
                ) %>% 
  dplyr::mutate(pas = pas %>% if_else(is.na(.), 0, .)
                ) %>% 
  group_by(dep
           ) %>% 
  dplyr::mutate(pos.new = pos - lag(pos, n = 1),
                pos.imp.new = pos.imp - lag(pos.imp, n = 1),
                pas.new = lag(pas, n = 1),
                smp.new = lag(smp, n = 1),
                ratio.new = signif(pos.new/smp.new), digits = 3,
                days.start =as.numeric(dat-first(dat), unit="days"),
                days.end = difftime(date, dat , units = c("days")),
                mav.pos.new = slide_dbl(pos.new, ~mean(.x, na.rm = TRUE), .before = 6))

dep <- dep %>%
  merge(pop %>% 
          select(dep = REGION, pop)) %>% 
  mutate(pos.hab = pos/pop*100000,
         smp.hab = smp/pop*100000,
         pos.new.hab = smp/pop*100000,
         mav.pos.new.hab = mav.pos.new/pop*1000000)

geom.dep <- dep %>% merge(shp, by.y = 'Departamento', by.x = 'dep', all.x = T) %>%
  st_as_sf(sf_column_name = 'geometry') 




c.dep <- geom.dep %>%
  dplyr::filter(dat == c.date)
```



```{r, message=F, warning=F}

vars_pmav_new <- dep %>%
  dplyr::select(dat,dep,mav.pos.new.hab) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(mav.pos.new.hab)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                                ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                       ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep

vars_mav_new <- dep %>%
  dplyr::select(dat,dep,mav.pos.new) %>% 
  dplyr::filter(dat == c.date) %>% 
  dplyr::arrange(dplyr::desc(mav.pos.new)) %>%
  dplyr::select(dep) %>%
  dplyr::mutate(dep = ifelse(dep=="LA LIBERTAD","LA_LIBERTAD",
                                ifelse(dep=="MADRE DE DIOS","MADRE_DE_DIOS",
                                       ifelse(dep=="SAN MARTIN","SAN_MARTIN",dep))))%>% 
  .$dep
```


```{r, message=F, warning=F}
nac1 <- nac %>%
  dplyr::mutate(RapidasPositivos = replace_na(RapidasPositivos,0),
                Descartados = replace_na(Descartados,0),
                PruebasRapidas = replace_na(PruebasRapidas,0),
                total_pos = Positivos + RapidasPositivos,
                pos_new = total_pos -lag(total_pos,default = 0),
                rapid_des = PruebasRapidas - RapidasPositivos,
                total_des = rapid_des + Descartados,
                des_new = total_des-lag(total_des,default = 0),
                Dia = ymd(Dia)) %>%
  dplyr::select(Dia,
                pos_new,
                des_new) %>%
  dplyr::mutate(cum_pos = cumsum(pos_new),
                tot_pruebas = pos_new+des_new,
                tm = difftime(date, Dia , units = c("days")))


nac3 <- nac1 %>%
  dplyr::mutate(new_cases = cum_pos - lag(cum_pos, default = 0),
                mav_new = slide_dbl(new_cases, ~mean(.x, na.rm = TRUE), .before = 6),
                max = max(mav_new)
  )

nac4 <- nac1 %>%
  dplyr::mutate(dias = as.numeric(Dia-first(Dia), unit="days"),
                calc = dias+20,
                dup_1 = exp((log(2)/1)*dias),
                dup_2 = exp((log(2)/2)*dias),
                dup_3 = exp((log(2)/3)*dias),
                dup_4 = exp((log(2)/4)*dias),
                mav_new = slide_dbl(pos_new, ~mean(.x, na.rm = TRUE), .before = 6)
  )

```


Casos Acumulados {.bg}
=====================================  

Column 1 {.tabset data-width=350} 
-------------------------------------

### Casos

```{r, message=F, warning=F}
labels.total <-  sprintf(
  "%s
Casos: %s",
  c.dep$dep, c.dep$pos) %>% lapply(htmltools::HTML)

pal.cases <- colorNumeric( palette="RdPu", domain = log(c.dep$pos), na.color="transparent")

leaflet(c.dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.cases(log(c.dep$pos)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.total,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal = pal.cases, values = log(c.dep$pos), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121) 
```

### Casos / 100k hab

```{r, message=F, warning=F}
labels.pos.hab <- sprintf(
  "%s
Casos/100k hab: %s",
  c.dep$dep, round(c.dep$pos.hab)) %>% lapply(htmltools::HTML)

pal.pos.hab <- colorNumeric( palette="RdPu", domain = log(c.dep$pos.hab), na.color="transparent")

leaflet(c.dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.pos.hab(log(c.dep$pos.hab)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.pos.hab,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal = pal.pos.hab, values = log(c.dep$pos.hab), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121) 
```


Column 2 {.tabset data-width=350} 
-------------------------------------

### Lineal

```{r, message=F, warning=F}
plot_ly(nac1) %>%
  add_trace(x = ~Dia, y = ~pos_new, 
            type = 'bar', name = 'Casos Nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~Dia, y = ~cum_pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados', 
            yaxis = 'y2',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Acumulados: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac1$pos_new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = 'Casos nuevos y acumulados - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de Reporte",
                      color = "white"),
         yaxis = list(side = 'left', title = 'Casos Nuevos por día (lineal)', 
                      showgrid = FALSE, zeroline = FALSE,
                      color = "white"),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Casos acumulados por día (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color = "white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=65, b=40, t=50),
         autosize=T
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = T
  )

```

### Logaritmico 

```{r, message=F, warning=F}
plot_ly(nac1) %>%
  add_trace(x = ~Dia, y = ~pos_new, 
            type = 'bar', name = 'Casos Nuevos',
            marker = list(color = '#006b7d'), 
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~Dia, y = ~cum_pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados', 
            yaxis = 'y2',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac1$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Casos Acumulados: %{y:.0f}
",
                                   '%{text}')) %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac1$pos_new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  ) %>% 
  layout(title = 'Casos nuevos y acumulados - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color ="white"),
         yaxis = list(side = 'left', title = 'Casos Nuevos por día (lineal)', 
                      showgrid = FALSE, zeroline = FALSE,
                      color="white"),
         yaxis2 = list(side = 'right', overlaying = "y", type = "log",
                       title = 'Casos acumulados por día (logaritmica)', 
                       showgrid = FALSE, zeroline = FALSE,
                       tickmode = "linear",
                       tick0 = 0,
                       color="white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",
                       x = 0.5,
                       y = -0.125,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=65, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines"),
         responsive = F
  )
```

### Duplicación

```{r, message=F, warning=F}
x <- data.frame(Dia = as.Date(seq(1,30, 1)+date)  )


y <- x %>%
  dplyr::mutate(dias = as.numeric(Dia-first(nac4$Dia), unit="days"),
                calc = dias+20,
                dup_1 = exp((log(2)/1)*dias),
                dup_2 = exp((log(2)/2)*dias),
                dup_3 = exp((log(2)/3)*dias),
                dup_4 = exp((log(2)/4)*dias)
  ) %>%
  bind_rows(nac4)

plot_ly(y)%>%
  add_trace(x = ~dias, y = ~pos_new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1') %>% 
  add_trace(x = ~dias, y = ~dup_1,
            mode = 'lines', 
            name = 'Casos se duplican en un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_2,
            mode = 'lines', 
            name = 'Casos se duplican en dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_3,
            mode = 'lines', 
            name = 'Casos se duplican en tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_4,
            mode = 'lines', 
            name = 'Casos se duplican en cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (4) días",
            hoverinfo = "text",
            legendgroup = 'group2')  %>% 
  layout(title = 'Total de casos acumulados desde el inicio de los casos',
         titlefont=list(color="white"),
         xaxis = list(title = "Días desde el primer reporte",
                      range = c(min(0),max(nac4$calc)+5),
                      color ="white"),
         yaxis = list(side = 'left', title = 'Total de casos acumulados', type="log",
                      range = c(min(0),max(6)),
                      showgrid = FALSE, zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.25,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=30, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```


Column 3 {.tabset data-width=350} 
-------------------------------------

### Acumulados - Lineal
```{r, message=F, warning=F}

last <- vars_mav_new[length(vars_mav_new)]
x <-  dep %>%
  select(dat,dep,pos) %>%
  spread(dep, pos) %>%
  mutate(tm = difftime(date, dat , units = c("days"))) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

```


```{r, message=F, warning=F}

plots <- lapply(vars_mav_new, function(var) {

last <- vars_mav_new[length(vars_mav_new)]

  plot_ly(x) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(x$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(x[var],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    ) %>%
    layout(xaxis = list(range = c(min(x$dat),
                                  max(x$dat)),
                        color = "white"),
           yaxis = list(color = "white"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Total de casos confirmados - Acumulado Lineal",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Total de casos confirmados",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Acumulados - Logaritmico
```{r, message=F, warning=F}

plots <- lapply(vars_mav_new, function(var) {

last <- vars_mav_new[length(vars_mav_new)]

  plot_ly(x) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(x$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(x[var],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    ) %>%
    layout(xaxis = list(range = c(min(x$dat),
                                  max(x$dat)),
                        color = "white"),
           yaxis = list(color = "white", type = "log", tickmode = "linear"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Total de casos confirmados - Acumulado Logarítmico",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Total de casos confirmados",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```


Casos Nuevos {.bg}
=====================================  

Column 1 {.tabset data-width=350} 
-------------------------------------
### Casos nuevos

```{r, message=F, warning=F}
labels.new <- sprintf(
  "%s
Casos: %s",
  c.dep$dep, c.dep$pos.new) %>% lapply(htmltools::HTML)

pal.newcases <- colorNumeric( palette="RdPu", domain = log(c.dep %>% dplyr::mutate(pos.new = ifelse(pos.new==0,NA, pos.new)) %>% .$pos.new), na.color="transparent")

leaflet(c.dep) %>%
  addTiles(urlTemplate = 'http://a.basemaps.cartocdn.com/dark_all/{z}/{x}/{y}.png',
           options = providerTileOptions(minZoom = 5, maxZoom = 6)) %>%
  addPolygons(fillColor = pal.newcases(log(c.dep$pos.new)),
              weight = 2,
              opacity = 1,
              color = "white",
              dashArray = "",
              fillOpacity = 0.7,
              highlight = highlightOptions(
                weight = 5,
                color = "#666",
                dashArray = "",
                fillOpacity = 0.7,
                bringToFront = TRUE),
              label = labels.new,
              labelOptions = labelOptions(
                style = list("font-weight" = "normal", padding = "3px 8px"),
                textsize = "15px",
                direction = "auto")) %>%
  addLegend("bottomleft", pal=pal.newcases, values = log(c.dep$pos.new), title= 'Casos', labFormat = labelFormat(transform = function(x) round(exp(x))))%>%
  setMaxBounds(lng1 = -90.648918,
               lat1 = 4.991423,
               lng2 = -59.605965,
               lat2 = -23.920121) 
```


Column 2 {.tabset data-width=350} 
-------------------------------------

### Diario y media móvil - Lineal

```{r, message=F, warning=F}
plot_ly(nac3) %>%
  add_trace(x = ~Dia, y = ~pos_new,
            type = 'scatter',
            mode = 'lines', name = 'Casos Nuevos por día',
            line = list(color = '#006b7d'), 
            text = paste(nac3$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~Dia, y = ~mav_new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Media Móvil de casos por día',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac3$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Media móvil: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac3$pos_new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = ' Casos nuevos por día y media móvil',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color="white"),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', showgrid = FALSE, zeroline = FALSE,
                      color = "white"),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Casos nuevos (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color="#ffa600",
                       range = c(min(0),
                                 max(nac3$pos_new))),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.15,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=0, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Media Móvil - logarítmica

```{r, message=F, warning=F}
plot_ly(nac3) %>%
  add_trace(x = ~Dia, y = ~pos_new,
            type = 'scatter', mode="lines",name = 'Casos Nuevos',
            line = list(color = '#006b7d'), 
            text = paste(nac3$tm, "días desde hoy"),
            hovertemplate = paste('Fecha: %{x}',
                                  '
Nuevos Casos: %{y}
',
                                  '%{text}'))%>% 
  add_trace(x = ~Dia, y = ~mav_new, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Media Móvil',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            text = paste(nac3$tm, "días desde hoy"),
            hovertemplate = ~paste('Fecha: %{x}',
                                   "
Media móvil: %{y:.0f}
",
                                   '%{text}'))  %>%
  add_segments(x = "2020-04-08", xend = "2020-04-08", 
               y = 0, yend=max(nac3$pos_new),
               text="2020-04-08",name="Inicio de P.R's",
               hovertemplate = paste('%{text}'),
               legendgroup = 'group2',
               width=2, 
               line = list(color = "#7aa82a", 
                           width = 3, 
                           dash = "dot")
  )%>% 
  layout(title = 'Media móvil (7d) y casos nuevos por día - Perú',
         titlefont=list(color="white"),
         xaxis = list(title = "Fecha de reporte",
                      color="white"),
         yaxis = list(side = 'left', title = 'Casos nuevos por día', showgrid = FALSE, zeroline = FALSE,
                      color = "white", type ="log"),
         yaxis2 = list(side = 'right', overlaying = "y",
                       title = 'Media móvil de casos nuevos - 7 días (lineal)', 
                       showgrid = FALSE, zeroline = FALSE,
                       color="#ffa600",
                       range = c(min(0),
                                 max(nac3$pos_new))),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.15,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=65, r=0, b=40, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Duplicación de la media móvil

```{r, message=F, warning=F}
x <- data.frame(Dia = as.Date(seq(1,30, 1)+date)  )


y <- x %>%
  dplyr::mutate(dias = as.numeric(Dia-first(nac4$Dia), unit="days"),
                calc = dias+20,
                dup_1 = exp((log(2)/1)*dias),
                dup_2 = exp((log(2)/2)*dias),
                dup_3 = exp((log(2)/3)*dias),
                dup_4 = exp((log(2)/4)*dias)
  ) %>%
  bind_rows(nac4)

plot_ly(y)%>%
  add_trace(x = ~dias, y = ~cum_pos, 
            type = 'scatter',
            mode = 'lines+markers', 
            name = 'Casos Acumulados',
            line = list(color = '#ffa600'), 
            marker = list(color = '#ffa600'),
            hovertemplate = ~paste("
Casos Acumulados: %{y:.d0}
"),
            legendgroup = 'group1') %>% 
  add_trace(x = ~dias, y = ~dup_1,
            mode = 'lines', 
            name = 'Casos se duplican en un (1) día',
            line = list(color = '#0e5871',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en un (1) día",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_2,
            mode = 'lines', 
            name = 'Casos se duplican en dos (2) días',
            line = list(color = '#006b7d',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en dos (2) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_3,
            mode = 'lines', 
            name = 'Casos se duplican en tres (3) días',
            line = list(color = '#007e7b',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (3) días",
            hoverinfo = "text",
            legendgroup = 'group2') %>% 
  add_trace(x = ~dias, y = ~dup_4,
            mode = 'lines', 
            name = 'Casos se duplican en cuatro (4) días',
            line = list(color = '#008f6a',
                        dash = "dash",
                        width=3.5),
            text = "Casos se duplican en tres (4) días",
            hoverinfo = "text",
            legendgroup = 'group2')  %>% 
  layout(title = 'Total de casos acumulados desde el inicio de los casos',
         titlefont=list(color="white"),
         xaxis = list(title = "Días desde el primer reporte",
                      range = c(min(0),max(nac4$calc)+5),
                      color ="white"),
         yaxis = list(side = 'left', title = 'Total de casos acumulados', type="log",
                      range = c(min(0),max(6)),
                      showgrid = FALSE, zeroline = FALSE,
                      tickmode = "linear",
                      tick0 = 0,
                      color ="white"),
         legend = list(orientation = "h",  
                       xanchor = "center",
                       yanchor = "bottom",  
                       x = 0.5,
                       y = -0.25,
                       font = list(color = "white")),
         paper_bgcolor="black",
         plot_bgcolor="black",
         hovermode = "closest",
         hoverdistance = 50,
         dragmode="pan",
         margin = list(l=50, r=50, b=30, t=50)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

```{r, message=F, warning=F}
x <-  dep %>%
  select(dat,dep,mav.pos.new) %>%
  spread(dep, mav.pos.new) %>%
  mutate(tm = difftime(date, dat , units = c("days"))) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 
y <- dep %>% #Distinto a deps2
  select(dat,dep,pos.imp.new) %>%
  spread(dep, pos.imp.new) %>%
  mutate(tm = difftime(date, dat , units = c("days")))%>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

colnames(y) <- paste(colnames(y), "2", sep = "_")

x<- y %>% 
  select(-c("dat_2")) %>% 
  cbind(x)

```


Column 3 {.tabset data-width=350} 
-------------------------------------

### Lineal
```{r, message=F, warning=F}

plots <- lapply(vars_mav_new, function(var) {

last <- vars_mav_new[length(vars_mav_new)]
x <-  dep %>%
  select(dat,dep,mav.pos.new) %>%
  spread(dep, mav.pos.new) %>%
  mutate(tm = difftime(date, dat , units = c("days"))) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 
y <- dep %>% #Distinto a deps2
  select(dat,dep,pos.imp.new) %>%
  spread(dep, pos.imp.new) %>%
  mutate(tm = difftime(date, dat , units = c("days")))%>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

colnames(y) <- paste(colnames(y), "2", sep = "_")

x<- y %>% 
  select(-c("dat_2")) %>% 
  cbind(x)

  plot_ly(x) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(x$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(y[paste0(var,"_2")],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(x$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last,TRUE,FALSE)) %>%
    layout(xaxis = list(range = c(min(x$dat),
                                  max(x$dat)),
                        color = "white"),
           yaxis = list(color = "white"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Media móvil (7 días) de casos nuevos",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Número de casos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```

### Logaritmica 
```{r, message=F, warning=F}

plots <- lapply(vars_mav_new, function(var) {

last <- vars_mav_new[length(vars_mav_new)]
x <-  dep %>%
  select(dat,dep,mav.pos.new) %>%
  spread(dep, mav.pos.new) %>%
  mutate(tm = difftime(date, dat , units = c("days"))) %>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 
y <- dep %>% #Distinto a deps2
  select(dat,dep,pos.imp.new) %>%
  spread(dep, pos.imp.new) %>%
  mutate(tm = difftime(date, dat , units = c("days")))%>% 
  dplyr::rename(LA_LIBERTAD = `LA LIBERTAD`,
                MADRE_DE_DIOS = `MADRE DE DIOS`,
                SAN_MARTIN = `SAN MARTIN`) 

colnames(y) <- paste(colnames(y), "2", sep = "_")

x<- y %>% 
  select(-c("dat_2")) %>% 
  cbind(x)

  plot_ly(x) %>%
    add_lines(x = ~dat, 
              y = as.formula(paste0("~", var)),
              text = paste(x$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Media Móvil: %{y:.2f}
',
                                    '%{text}'),
              name = ifelse(var == last,"Media Móvil",var),
              legendgroup = 'group1',
              showlegend = ifelse(var == last,TRUE,FALSE), 
              line = list(color = "#ffa600", 
                          width = 4)
    ) %>%
    add_segments(x = "2020-04-08", xend = "2020-04-08", 
                 y = 0, yend = max(y[paste0(var,"_2")],na.rm = T),
                 text="2020-04-08", name="Inicio de P.R's",
                 hovertemplate = paste('%{text}'),
                 legendgroup = 'group2',
                 showlegend = ifelse(var == last,TRUE,FALSE), 
                 line = list(color = "#7aa82a", 
                             width = 3, 
                             dash = "dot")
    )%>%
    add_trace(x = ~dat, y = as.formula(paste0("~", var,"_2")),
              type = 'bar', name = 'Casos Nuevos',
              marker = list(color = '#006b7d'), 
              text = paste(x$tm, "días desde hoy"),
              hovertemplate = paste('Fecha: %{x}',
                                    '
Nuevos Casos: %{y}
',
                                    '%{text}'),
              showlegend = ifelse(var == last,TRUE,FALSE)) %>%
    layout(xaxis = list(range = c(min(x$dat),
                                  max(x$dat)),
                        color = "white"),
           yaxis = list(color = "white", type="log"),
           annotations = list(text = ifelse(var=="LA_LIBERTAD","LA LIBERTAD",
                                            ifelse(var=="MADRE_DE_DIOS","MADRE DE DIOS",
                                                   ifelse(var=="SAN_MARTIN","SAN MARTIN",paste0("",var,"")))),
                              x = 0,y = 1.15,
                              yref = "paper",xref = "paper",
                              xanchor = "left",yanchor = "top",
                              showarrow = FALSE,
                              font = list(size = 16,
                                          color = "white")),
           paper_bgcolor="black",
           plot_bgcolor="black",
           legend = list(orientation = "h",  
                         xanchor = "center",
                         yanchor = "bottom",
                         x = 0.5,
                         y = -0.125,
                         font = list(color = "white")),
           showlegend =T)
})

subplot(plots,nrows=5, shareX = T, titleX = F) %>%
  layout(title = list(text = "Media móvil (7 días) de casos nuevos",
                      font = list(size = 24,
                                  color="white")),
         annotations = list(
           list(text = "Fecha de reporte",
                x = 0.5,
                y = -0.09,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color = "white")),
           list(text = "Media móvil - Número de casos",
                x = -0.05,
                y = 0.5,
                yref = "paper",
                xref = "paper",
                showarrow = FALSE,
                font = list(size = 16,
                            color ="white"),
                textangle = -90)),
         hovermode = "closest",
         hoverdistance = 10,
         dragmode="pan",
         margin = list(l=75, r=0, b=65, t=60)
  ) %>%
  config(locale = "es",
         displaylogo=F,
         modeBarButtonsToRemove = c("select2d","zoom2d","lasso2d",
                                    "drawclosedpath","drawopenpath",
                                    "hoverClosestCartesian","hoverCompareCartesian",
                                    "toggleHover","toggleSpikelines")
  )

```


Fallecidos {.bg}
===================================== 

Column 1 {.tabset data-width=350} 
-------------------------------------



Column 1 {.tabset data-width=350} 
-------------------------------------



Column 1 {.tabset data-width=350} 
-------------------------------------

Fallecidos Nuevos {.bg}
===================================== 


Diagnósticos {.bg}
===================================== 



Diagnósticos Nuevos {.bg}
=====================================